To generate synthesized arrays with known differentially phosphorylated peptides, we need a procedure to artificially phosphorylate or dephosphorylate a predetermined subset of peptides on an array. Here we propose a procedure to do this to array Y, which is an inter-array technical replicate of X, producing Y′. The procedure is described in technical detail in Algorithm 2 as the basis for rapid implementation. Algorithm 2 Artificial Phosphorylation/Dephosphorylation
 Input:A={A1,⋯,An}, X, Y, peptideIndex, phosphorylated, T, α
 Output: Y′
 Create measurement repository set R R=ri,j∣1≤i≤n,1≤j≤mri,j={pi,j,k∣1≤k≤l}
 where ri,j is the set of all intra-array replicates of the jth peptide of Ai
 Y′← a copy of Y
 q←1
 while (q≤ length(peptideIndex)) do
  t←peptideIndex[q]
  abct←∑k=1lFxt,k−Bxt,kl
  if abct≤0 then
   v=abctT
   w=abct×T
  else
   v=T×abct
   w=abctT
  end if
  if (phosphorylated[t] =1) then
   if (there is a ri,j∈R where the mean of ri,j is statistically bigger than v, considering a significance level of α) then
    yt′←ri,j
   else
    Report tth peptide as a non-differentially phosphorylated peptide
   end if
  else
   if (there is a ri,j∈R where the mean of ri,j is statistically less than w, considering a significance level of α) then
    yt′←ri,j
   else
    Report tth peptide as a non-differentially phosphorylated peptide
   end if
  end if
  q←q+1
 end while
 return Y′